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- PDB-4j8a: Irradiated-state structure of sfGFP containing the unnatural amin... -

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Basic information

Entry
Database: PDB / ID: 4j8a
TitleIrradiated-state structure of sfGFP containing the unnatural amino acid p-azido-phenylalanine at residue 145
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta-barrel / chromophore by cyclisation / p-azido-L-phenylalanine / cytosol
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsReddington, S.C. / Jones, D.D. / Rizkallah, P.J. / Tippmann, E.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Different Photochemical Events of a Genetically Encoded Phenyl Azide Define and Modulate GFP Fluorescence.
Authors: Reddington, S.C. / Rizkallah, P.J. / Watson, P.D. / Pearson, R. / Tippmann, E.M. / Jones, D.D.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jan 22, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,44738
Polymers27,8861
Non-polymers2,56137
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.500, 58.700, 91.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 27886.352 Da / Num. of mol.: 1
Mutation: S30R, Y39N, Q80R, F99S, N105T, F145(HOX), M153T, V163A, A171V, A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / References: UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION, DELETION, OR INSERTION OF RESIDUES F64, S65, Y66, G67 WERE INTRODUCED TO FORM CHROMOPHORE ...MUTATION, DELETION, OR INSERTION OF RESIDUES F64, S65, Y66, G67 WERE INTRODUCED TO FORM CHROMOPHORE CRO 66. RESIDUES SER 65, TYR 66, GLY 67 FORM A CHROMOPHORE CRO 66

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 10 mg/mL protein and 100 mM Tris-HCl, pH 8.3, 2 M (NH4)2SO4, 200+200 nanoL drop against 60 microL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 19, 2012 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.26→46.5 Å / Num. all: 67853 / Num. obs: 67853 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 16

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.26→14.79 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.357 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1646 3429 5.1 %RANDOM
Rwork0.1287 ---
all0.1305 67742 --
obs0.1305 67742 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100 Å2 / Biso mean: 23.5069 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2---0.27 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.26→14.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 158 260 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192220
X-RAY DIFFRACTIONr_bond_other_d0.0030.022116
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0042966
X-RAY DIFFRACTIONr_angle_other_deg0.67234869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5935269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00225.149101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86315351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.902159
X-RAY DIFFRACTIONr_chiral_restr0.0620.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022480
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02499
X-RAY DIFFRACTIONr_rigid_bond_restr8.85132074
X-RAY DIFFRACTIONr_sphericity_bonded16.78552016
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 243 -
Rwork0.251 4657 -
all-4900 -
obs--98.57 %

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